Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985

Obasa, Adetayo Emmanuel; Engelbrecht, Susan; Jacobs, Graeme Brendon

doi:10.1038/s41598-019-42417-1

Cited by 8 publications

(5 citation statements)

References 29 publications

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“…To improve the knowledge of the HIV-1 transmission dynamics in the state of São Paulo, Brazil, this study considered a large dataset that examines the demographic and clinical characteristics of individuals infected by the subtypes B, C and F1. The observed prevalence of HIV-1 subtypes was similar to that observed in previous studies in the region being the epidemic was driven by subtype B, followed by subtype F and the less frequent, subtype C ( 21 ). However, when only patients with recent diagnoses (between January 2013 and February 2015) are considered, the frequency of subtype C is about 10%.…”

Section: Discussionsupporting

confidence: 88%

Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil

Pimentel,

Pineda-Peña,

Sebastião

et al. 2024

Front. Public Health

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BackgroundMolecular epidemiology techniques allow us to track the HIV-1 transmission dynamics. Herein, we combined genetic, clinical and epidemiological data collected during routine clinical treatment to evaluate the dynamics and characteristics of transmission clusters of the most prevalent HIV-1 subtypes in the state of São Paulo, Brazil.MethodsThis was a cross-sectional study conducted with 2,518 persons living with HIV (PLWH) from 53 cities in São Paulo state between Jan 2004 to Feb 2015. The phylogenetic tree of protease/reverse transcriptase (PR/RT) regions was reconstructed by PhyML and ClusterPicker used to infer the transmission clusters based on Shimodaira–Hasegawa (SH) greater than 90% (phylogenetic support) and genetic distance less than 6%.ResultsOf a total of 2,518 sequences, 2,260 were pure subtypes at the PR/RT region, being B (88%), F1 (8.1%), and C (4%). About 21.2% were naïve with a transmitted drug resistance (TDR) rate of 11.8%. A total of 414 (18.3%) of the sequences clustered. These clusters were less evident in subtype B (17.7%) and F1 (15.1%) than in subtype C (40.2%). Clustered sequences were from PLWH at least 5 years younger than non-clustered among subtypes B (p < 0.001) and C (p = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; p < 0.05). The TDR rate in clustered patients was 15.4, 13.6, and 3.1% for subtypes B, F1, and C, respectively. Most of the infections in subtypes B (80%), C (64%), and F1 (59%) occurred within the state of São Paulo. The metropolitan area of São Paulo presented a high level of endogenous clustering for subtypes B and C. The São Paulo city had 46% endogenous clusters of subtype C.ConclusionOur findings showed that MSM, antiretroviral therapy in Treatment-Naive (ART-naïve) patients, and HIV1-C, played an important role in the HIV epidemic in the São Paulo state. Further studies in transmission clusters are needed to guide the prevention intervention.

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Section: Discussionsupporting

confidence: 88%

Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil

Pimentel,

Pineda-Peña,

Sebastião

et al. 2024

Front. Public Health

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“…To understand the divergence time and evolutionary time scale of 10 HIV-1 sequences obtained with NGS, molecular clock analysis with Bayesian inference was performed with BEAST v2.6 (burn-in = 25%) 52 . For Bayesian inference, the two most early genomic HIV-1 sequences (MN082768 53 and KJ704791 54 ) were included in the genomic sequence alignment, which was used in the genomic phylogenetic analysis above. Based on a previous study on the origin time and the evolutionary time scale of HIV-1 with partial sequence fragments of gag , pol , and env genes 55 , a relaxed clock lognormal clock model and a coalescent Bayesian skyline tree model were selected with MCMC 10,000,000 generation for the inference.…”

Section: Methodsmentioning

confidence: 99%

Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

Ryou

Yoo

Kim

et al. 2021

Sci Rep

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In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.

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“…In clinical settings, Sanger bulk sequencing is the most common and widely used for HIV drug resistance testing. The limitation of the Sanger bulk sequencing method is that it can only detect variants with prevalence > 20% which is well known [32][33][34]. Studies have described the presence of minority HIV-1 drug resistance mutations in treatment-naïve patients which could potentially impact treatment outcome [4,13,16,19,35].…”

Section: Introductionmentioning

confidence: 99%

Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa

et al. 2021

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Background HIV-1C has been shown to have a greater risk of virological failure and reduced susceptibility towards boosted protease inhibitors (bPIs), a component of second-line combination antiretroviral therapy (cART) in South Africa. This study entailed an evaluation of HIV-1 drug resistance-associated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients on the South African national second-line cART regimen receiving bPIs. Methods During 2017 and 2018, 67 patient samples were sequenced using high-throughput sequencing (HTS), of which 56 samples were included in the final analysis because the patient’s treatment regimen was available at the time of sampling. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were amplified and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Drug Resistance Database. Results Statistically significantly higher PI RAMs were observed in minor viral quasispecies (25%; 14/56) compared to non-nucleoside reverse transcriptase inhibitors (9%; 5/56; p = 0.042) and integrase inhibitor RAM (4%; 2/56; p = 0.002). The majority of the drug resistance mutations in the minor viral quasispecies were observed in the V82A mutation (n = 13) in protease and K65R (n = 5), K103N (n = 7) and M184V (n = 5) in reverse transcriptase. Conclusions HTS-GRT improved the identification of PI and reverse transcriptase inhibitor (RTI) RAMs in second-line cART patients from South Africa compared to the conventional GRT with ≥20% used in Sanger-based sequencing. Several RTI RAMs, such as K65R, M184V or K103N and PI RAM V82A, were identified in < 20% of the population. Deep sequencing could be of greater value in detecting acquired resistance mutations early.

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Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985

Cited by 8 publications

References 29 publications

Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil

Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil

Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa

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